人类和黑猩猩Y染色体结构和基因含量的差异性

解读人类和黑猩猩之间的差异性对于研究人类的进化历史具有非常重要的意义。人类和黑猩猩Y染色体相继测序完毕,利用dot-plot程序可以分析它们之间的差异性。研究结果显示,人类和黑猩猩MSY区在结构和基因含量上有很大的差异,人类MSY常染色质主要由扩增序列、X退化序列和X转座序列组成,而黑猩猩MSY常染色质主要由扩增序列和X退化序列组成。黑猩猩的MSY区含有19个回文序列,而人类只有8个回文序列。黑猩猩MSY区的基因只包含了人类MSY区基因的三分之二。通过分析可以推测,黑猩猩和人类MSY之间的显著差异主要来源于四个因素的协同作用:MSY在精子生成中的主要作用;MSY区内频繁的异常重组;减数分裂交叉重组中的"遗传便车"效应;配偶行为引起的精子的竞争。综合比较黑猩猩和人类Y染色体结构和基因含量将对研究Y染色体的进化历史及其动力产生非常重要的意义。     

草鱼诱导型一氧化氮合酶cDNA和启动子的克隆及分析

应用PCR和RACE技术,以细菌脂多糖(LPS)刺激的草鱼头肾白细胞cDNA为模板,获得草鱼iNOS (Inducible nitric oxide synthase)全长cDNA序列.该序列共4286 bp,编码含1080个氨基酸残基的蛋白.氨基酸序列比对分析发现草鱼iNOS与金鱼iNOS a和b、斑马鱼iNOS 2b以及鲤鱼iNOS高度保守,序列一致性均大于80%;它们的血红素、四氢生物蝶呤、钙调蛋白、FMN、FAD和NADH等辅因子结合区域也十分保守.用NJ法对新获得的序列和其它脊椎动物NOS的编码序列进行进化分析证实它属于诱导型NOS.在此基础上,运用基因步移技术分离草鱼iNOS基因的启动子序列,共有1978 bp.生物信息学分析发现该序列含有包括GR、AP1、C/EBP、ER、YY1、IRF1和IL-6 REBP在内的多个转录因子的潜在结合位点.     

基因文库的鉴定和应用

由于草菇是一种同宗结合的食用真菌,这给草菇的杂交育种带来了一定的困难。本文在建立草菇部分基因文库的基础之上,对草菇的基因文库进行了鉴定。在草菇基因文库中任意抽取72个克隆,利用专一的PCR方法,测出在草菇基因文库中,草菇基因组DNA的平均大小为1156个碱基对。在基因文库中任意选择53个克隆,利用专一的PCR进行DNA扩增以及dig非同位素标记,用于和草菇基因组DNA杂交。在测试的53个克隆中有8％的高度重复序列,36％中度重复序列和56％的低度重复序列。     

秦巴山区漆树nrDNAITS和cpDNA序列分子进化特点的分析

应用PCR产物直接测序法分析漆树种群nrDNA （核糖体DNA） ITS序列和cpDNA序列（matK、rbcL、psbA-trnH）的碱基差异,初步研究两套植物基因组的变异速率。结果表明：nrDNA ITS序列共有518 bp,有变异位点15处,变异位点百分率为2.9%,（G+C）含量为61.8%。cpDNA序列合并后长度1 907 bp,有变异位点20处,变异位点百分率为1.05%,（G+C）含量为36.1%。通过对ITS序列核糖型（Ribotype）和叶绿体序列单倍型（Haploype）进行分析发现,秦巴山区漆树区域性分布明显,不同区域拥有自己独特的单倍型,漆树居群历史近期没有扩张。nrDNA ITS序列较叶绿体序列进化较快,变异速率较快。nrDNA ITS序列及叶绿体matK、psbA-trnH适合漆树的亲缘地理学研究。     

毕氏酵母胱硫醚合成酶基因的克隆和序列分析

胱硫醚合酶（cystathione beta-synthase,CBS）是半胱氨酸代谢中一个重要的酶。以PCR技术为主,克隆了毕氏酵母来源的CBS基因。首先基于不同来源的CBS基因的序列比对,设计了一对CBS的性简并引物,用它扩增出毕氏酵母CBS基因的一个保守片段。根据这段DNA的序列,设计了5′RACE和3′RACE的引物,分别克隆了该基因的3′区和5′区。由此装配出完整的毕氏酵母的CBS基因序列。该基因编码了一种501个氨基酸残基的蛋白质。核苷酸序列和氨基酸序列的排比显示该基因与酿酒酵母来源的CBS基因有较高的相似性。破坏该基因,造成毕氏酵母的半胱氨酸生长依赖性。该序列已存入GenBank／EBM／DDBJ数据库,其登录号为No.AF367364。     

质粒pXZ10145核苷酸序列测定和分析

以Sanger双脱氧中止法为原理,利用美国ABI公司370A自动核酸序列分析仪,我们测定了谷氨酸棒杆菌质粒pxzl0145全长4887bp的核苷酸序列,该质粒上存在包括ApaI等18种限制酶的单一切点,其它限制酶切点的数目和位置也被定出,质粒上有8个可能的阅读框架,通过序列分析,我们确定了pxzlO145断裂生成缺失突变体pNAT65的两侧位点,在两个断裂点上发现存在“ATCTAGC”7个碱基的同向重复序列。     

外显子和内含子的序列复杂性

引入了两个新的关于序列复杂性的测度,并以此为指标分析比较了结构基因序列中的外显子和内含子的复杂性差异。     

窄叶鲜卑花(Sibiraea angustata)nrDNA ITS和cpDNA trnL-F序列分子进化特点的分析

应用PCR产物直接测序法分析了窄叶鲜卑花居群间nrDNA(核糖体DNA)ITS序列和cpDNA(叶绿体DNA)trnL-F的碱基差异,并与cpDNAtrnS-G序列和rpl20-rps12序列进行比较,从而初步研究两套植物基因组的变异速率。采用改良的CTAB法从硅胶干燥的窄叶鲜卑花叶片中提取总DNA,并对nrDNA ITS和cpDNAtrnL-F区域进行扩增、纯化、测序。nrDNA ITS序列共有601 bp,有变异位点3处,变异位点百分率为0.05%,(G+C)含量为41.4%。cpDNAtrnL-F序列共有927 bp,有变异位点1处,变异位点百分率0.01%,(G+C)含量为32.6%,两种序列的核苷酸多样性非常低。比较发现,窄叶鲜卑花nrDNA ITS区域较cpDNAtrnS-G序列和rpl20-rps12序列保守,变异速率较慢,比cpDNAtrnL-F序列变异速率稍快。通过对ITS序列单倍型(haplotype)进行分析发现,窄叶鲜卑花现有分布范围经历了居群近期范围扩张,与叶绿体基因组(trnS-G和rpl20-rps12序列)得出的结论一致。因此,窄叶鲜卑花nrDNA ITS序列适合该种的谱系地理学研究。     

蜱传脑炎病毒东北株E蛋白的核酸和氨基酸序列

从我国东北林区死者脑组织中,分离到蜱传脑炎病毒ＨＬＪ－１株,测定了它的Ｅ蛋白基因序列和推导的氨基酸序列,以及Ｅ蛋白抗原位点反应图谱。将该株与远东亚型Ｓｏｆｙｎ株和中欧亚型Ｎｅｕｄｅｒｆｌ株做了同源性比较,ＨＬＪ－１株与Ｓｏｆｙｎ株Ｅ蛋白基因的核苷酸及氨基酸的同源性分别为９４．３％和９８．８％;与Ｎｅｕｄｏｅｒｆｌ的核苷酸和氨基酸的同源性分别为８３．７％和９６％。在Ｅ蛋白的核苷酸序列中,ＨＬＪ－１和     

秦岭羚牛高度重复序列DNA片段的分子克隆和序列分析

羚牛（Budorcas taxicolor)属偶蹄目（Artiodactyla)、牛科（Bovidae),为我国一类大型珍贵保护动物。我们从其基因组中克隆得到若干约800bp的BamHI高度重复序列并对部分克隆进行了序列测定,发现它们显示了很高的同源性。利用其中一个单元为探针,对限制酶消化后的羚牛基因组DNA作杂交分析,发现其杂交谱带不具有个体及亚种间特异性,说明该重复序列在羚牛基因组中具有保守的分布和排列。在牛科动物中,羚牛BamHI片段与绵羊属和山羊属的相关序列具有高度同源性,而与水牛和家牛序列差异较大。这些结果为羚牛与羊亚科物种亲源关系较近的分类学观点提供了分子生物学证据。有证据表明,这些片段可能代表羚牛染色体着丝点的卫星DNA单体。     

Virus-associated human tumors: cervical carcinomas and papilloma viruses

The latest experimental data on the role of viruses in the origin of human tumors are discussed. This group of viruses consists of T-cell leukemia virus type 1 (HTLV 1), herpes viruses (HHV 8 and Epstein-Barr virus), hepatitis B virus, and human papilloma viruses. The most typical feature of this group of viruses is a very long latent period from the initial infection to the development of the disease that varies between 10 and 40 years. The mechanism of malignant cell conversion is specific for each viral type but is mainly associated with a disruption of functions of cellular genes participating in the control of cell division and proliferation. It can be a direct inactivation of tumor suppressor genes by their interaction with viral gene products (papilloma viruses), or a trans-activation of cellular genes modulating cell proliferation by viral gene products (hepatitis B virus and HTLV 1). Viruses play an initiative role and additional genetic changes in the genome of infected cells are necessary for complete expression of the oncogenic potential of the viral genes. Only these cells will give rise to a monoclonal cell population with uncontrolled proliferation. New approaches for the creation of vaccines against cancers associated with hepatitis B virus and papilloma viruses (hepatocellular carcinomas and cervical tumors, respectively) are in progress. These vaccines have been found to be effective in prevention of the disease in the experimental models and are now beginning to be used for human vaccination.     

Inactivation kinetics of model and relevant blood-borne viruses by treatment with sodium hydroxide and heat.

To determine the efficacy of a clean-in-place system for the inactivation of viruses present in human plasma, the effect of 0.1 M sodium hydroxide at 60 degrees C on viral infectivity was investigated. Inactivation of the following model and relevant viruses were followed as a function of time: human hepatitis A virus (HAV), canine parvovirus (CPV; a model for human parvovirus B-19) pseudorabies virus (PRV, a model for hepatitis B virus), and bovine viral diarrhoea virus (BVDV, a model for hepatitis C virus and human immunodeficiency virus). Infectivity of CPV was determined by a novel in situ EIA method which will prove useful for studies to validate parvovirus inactivation or removal. Infectivity of BVDV, PRV and CPV were shown to be reproducibly inactivated below the limit of detection by 0.1 M NaOH at 60 degrees C within 30 s. HAV was inactivated to below the limit of detection within 2 min. Treatment with heat alone also resulted in some log reduction for all viruses tested except for CPV which remained unaffected after heating at 60 degrees C for 16 min. Treatment of HAV with hydroxide alone (up to 1.0 m) at 15 degrees C did not lead to rapid inactivation. Collectively, these data suggest that 0.1 M NaOH at 60 degrees C for two min should be sufficient to inactivate viruses present in process residues.     

Viral metagenome analysis to guide human pathogen monitoring in environmental samples

Aims: The aim of this study was to develop and demonstrate an approach for describing the diversity of human pathogenic viruses in an environmentally isolated viral metagenome. Methods and Results: In silico bioinformatic experiments were used to select an optimum annotation strategy for discovering human viruses in virome data sets and applied to annotate a class B biosolid virome. Results from the in silico study indicated that <1% errors in virus identification could be achieved when nucleotide‐based search programs (BLASTn or tBLASTx), viral genome only databases and sequence reads >200 nt were considered. Within the 51 925 annotated sequences, 94 DNA and 19 RNA sequences were identified as human viruses. Virus diversity included environmentally transmitted agents such as parechovirus, coronavirus, adenovirus and aichi virus, as well as viruses associated with chronic human infections such as human herpes and hepatitis C viruses. Conclusions: This study provided a bioinformatic approach for identifying pathogens in a virome data set and demonstrated the human virus diversity in a relevant environmental sample. Significance and Impact of the Study: As the costs of next‐generation sequencing decrease, the pathogen diversity described by virus metagenomes will provide an unbiased guide for subsequent cell culture and quantitative pathogen analyses and ensures that highly enriched and relevant pathogens are not neglected in exposure and risk assessments.     

Physical, chemical and morphologic dimensions of human hepatitis A virus strain CR326 (38578).

CR326 human hepatitis A virus purified by isopycnic banding from infected marmoset sera was shown to consist of 27 nm spherical particles on electron microscopic examination. The particles were identified as hepatitis A virus by tests for infectivity and by specific neutralization of infectivity with convalescent human hepatitis A serum. Also, indentical 27 nm viruses in liver extracts gave specific reactions with hepatitis A antisera when tested by immune electron microscopy. The bouyant density of the virus in CsCl was 1.34 and it was heat (60 degrees), ether and acid stable but was destroyed by heat (100 degrees), formalin (1:4000) and ultraviolet irradiation. Electron microscopic studies of sections of infected marmoset liver showed intracytoplasmic virus particles, usually in vesicles. Presumptive findings for RNA, together with the intracytoplasmic location of the virus, indicated the virus to be of RNA-type. The attributes of the virus indicate it is closely related to the enterovirus family and not to hepatitis B virus.     

Cyclophilin A and viral infections

Cyclophilin A (CyPA) is a peptidyl-prolyl cis/trans isomerase originally identified as the target of the immunosuppressive drug cyclosporine A. A number of reports have demonstrated that CyPA plays a critical role in the successful replication of viruses such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), hepatitis B virus (HBV), etc. However, recent studies demonstrated that CyPA also possesses a repressive effect on the replication of some viruses like Influenza A virus and rotavirus. Moreover, CyPA could also regulate host IFN-I response to viral infections. Together, these evidences showed diverse roles of CyPA in viral infection.     

Inhibition of virus replication by RNA interference

RNA interference (RNAi) is a sequence-specific gene-silencing mechanism in eukaryotes, which is believed to function as a defence against viruses and transposons. Since its discovery, RNAi has been developed into a widely used technique for generating genetic knock-outs and for studying gene function by reverse genetics. Additionally, inhibition of virus replication by means of induced RNAi has now been reported for numerous viruses, including several important human pathogens such as human immunodeficiency virus type 1, hepatitis C virus, hepatitis B virus, dengue virus, poliovirus and influenza virus A. In this review, we will summarize the current data on RNAi-mediated inhibition of virus replication and discuss the possibilities for the development of RNAi-based antiviral therapeutics.     

Viral internal ribosome entry site structures segregate into two distinct morphologies

An increasing number of viruses have been shown to initiate protein synthesis by a cap-independent mechanism involving internal ribosome entry sites (IRESs). Predictions of the folding patterns of these RNA motifs have been based primarily on sequence and biochemical analyses. Biophysical confirmation of the models has been achieved only for the IRES of hepatitis C virus (HCV), which adopts an open structure consisting of two major stems. We have conducted an extensive comparison of flavivirus and picornavirus IRES elements by negative stain transmission electron microscopy. All of the flavivirus IRESs we examined (those of GB virus-B, GB virus-C, and classical swine fever virus) fold to give a structure similar to that of the HCV IRES, as does an IRES recently found on mRNA encoded by human herpesvirus 8. The larger picornavirus IRESs (those of foot-and-mouth disease virus, rhinovirus, encephalomyocarditis virus, and hepatitis A virus) are morphologically similar, comprising a backbone with two protruding stems, and distinct from the flavivirus IRESs.     

Molecular structure of the Japanese hepatitis C viral genome

The amino acid sequence of the polyprotein deduced from the nucleotide sequence of the Japanese hepatitis C virus genome (N. Kato et. al. (1990) Proc. Natl. Acad. Sci. USA 87, 9524–9528)indicated that this virus is a member of a new class of positive-stranded RNA viruses. Several domains of this polyprotein also showed weak homology with those of flaviviruses and pestiviruses including the chymotrypsin-like serine proteinase. NTPase and RNA-dependent RNA polymerase     

Transfusion-transmitted infectious diseases

A spectrum of blood-borne infectious agents is transmitted through transfusion of infected blood donated by apparently healthy and asymptomatic blood donors. The diversity of infectious agents includes hepatitis B virus (HBV), hepatitis C virus (HCV), human immunodeficiency viruses (HIV-1/2), human T-cell lymphotropic viruses (HTLV-I/II), Cytomegalovirus (CMV), Parvovirus B19, West Nile Virus (WNV), Dengue virus, trypanosomiasis, malaria, and variant CJD. Several strategies are implemented to reduce the risk of transmitting these infectious agents by donor exclusion for clinical history of risk factors, screening for the serological markers of infections, and nucleic acid testing (NAT) by viral gene amplification for direct and sensitive detection of the known infectious agents. Consequently, transfusions are safer now than ever before and we have learnt how to mitigate risks of emerging infectious diseases such as West Nile, Chikungunya, and Dengue viruses.     

利用寡核苷酸微阵列技术对HBV、HCV、HIV、HAV、GBV-C/HGV和B19进行同时监测的初步研究

探讨研制能同时检测HBV、HCV、HIV、HAV、GBV-C/HGV和B19的微阵列监控芯片。根据病毒公开发表序列,序列比对,得出保守区域,设计病毒的特异性检测探针,同时设置阴性、阳性参照探针,制备监控微阵列。利用随机引物PCR方法标记样品中的病毒靶序列,标记产物与微阵列上的探针杂交,清洗、扫描后进行结果分析。通过对质粒或模式分子的检测以及经HBV、HCV、HIV临床标本的验证,发现该微阵列监控芯片具有良好的特异性。其对质粒的检测灵敏度可达102病毒拷贝数,对临床标本的检测灵敏度可达103病毒拷贝数。此外,该微阵列监控芯片可检测出病毒混合感染血清。为微阵列监控芯片应用于此六种血液病毒的检测打下一定的基础。